nextflow.config

manifest {
  author = 'James Zlosnik'
  name = 'bbmap-nf'
  version = '0.0.1'
  description = 'BCCDC-PHL bbmap'
  mainScript = 'main.nf'
  nextflowVersion = '>=20.01.0'
}

params {
  profile = false
  cache = ''
  outdir = 'results'
  illumina_suffixes = ['*_R{1,2}_001', '*_R{1,2}', '*_{1,2}' ]
  fastq_exts = ['.fastq.gz', '.fq.gz', '.fastq', '.fq']
  fastq_search_path = makeFastqSearchPath( illumina_suffixes, fastq_exts )
  target_depth = 200
  min_depth = 5
}

def makeFastqSearchPath ( illumina_suffixes, fastq_exts ) {
    def fastq_search_path = []
    for (suffix in illumina_suffixes){
        for (ext in fastq_exts) {
            fastq_search_path.add(params.fastq_input.toString() + '/' + suffix.toString() + ext.toString())
        }
    }
    return fastq_search_path
}

profiles {
  conda {
    process.conda = "$baseDir/environments/environment.yml"
    if (params.cache) {
      conda.cacheDir = params.cache
    }
  }
}

process {
  withName: bbmap {
    cpus = 4
  }
}